How can I restore Ctrl+<key> functionality in Microsoft Keyboard Layout Creator?
You need to modify the .klc file manually.
Basically you just modify the VK_ column to match the value in column 1.
So for example if you want to bind L to N, you would create the keyboard as you normally would in KLC. Then you would open the KLC file in a text editor. Find the value L in the VK_ column, and switch it to an N.
For more information, I wrote the complete steps on my blog.